Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

(How to) Run germline single sample short variant discovery in DRAGEN mode Follow


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    Hi, I can't seem to find the str file, would you please check the resource bundle? Thanks

    I used this link to search:


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    Hi, is this the complete workflow?

    I would perform trimming before mapping.

    Also is Picards MarkDuplicates no longer necessary?

    How to convert sam to bam files?

    Can I use the workflow for exome data?

    Thank you!

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    Luc Marchand

    The google links seems obsolete.  The reference hash table files are not there either.

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